bug fix in mcmc.popsize()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@138 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/ChangeLog b/ChangeLog
index 94d9816f25afd2f3ca0a76b58d2918b99f01788e..2858cd498b2c2f10943e0200468b45528a04bb1e 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -18,6 +18,9 @@ BUG FIXES
     o dist.nodes() returned duplicated column(s) with unrooted and/or
       multichotomous trees.
 
+    o mcmc.popsize() terminated unexpectedly if the progress bar was
+      turned off.
+
 
 
                CHANGES IN APE VERSION 2.6-1

diff --git a/DESCRIPTION b/DESCRIPTION
index f007b94050f0ed70c9f0a925f38547f99e6a1259..b9d0974b4df82717559bc0986db7629c114a7b2c 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.6-2
-Date: 2010-11-15
+Date: 2010-11-18
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>

diff --git a/R/mcmc.popsize.R b/R/mcmc.popsize.R
index 35670a9c27303183c4ec9cd64bc5f382a958551a..22dafff75fc304eb4fdf2b8652ca2e5e0b208fc1 100644 (file)
--- a/R/mcmc.popsize.R
+++ b/R/mcmc.popsize.R
@@ -1,11 +1,11 @@
-## mcmc.popsize.R (2004-12-02)
+## mcmc.popsize.R (2010-11-16)
 
 ##   Run reversible jump MCMC to sample demographic histories
 
-## Copyright 2004 Rainer Opgen-Rhein and Korbinian Strimmer
+## Copyright 2004-2010 Rainer Opgen-Rhein and Korbinian Strimmer
 
 ## Portions of this function are adapted from rjMCMC code by
-## Karl Broman (see http://www.biostat.jhsph.edu/~kbroman/)
+## Karl W Broman (see http://www.biostat.wisc.edu/~kbroman/)
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -160,14 +160,17 @@ mcmc.popsize <-
 
  #BEGIN CALCULATION
 
-  for(i in (1:nstep + 1)) {
-
-  #progress bar
-  if(i %% 100 == 0){
-   z<-i/nstep
-   zt<-(i-100)/(nstep)
-   polygon(c(zt,zt,z,z), c(1,0,0,1), col="black")
-
+  for(i in (1:nstep + 1)) 
+  {
+    #progress bar
+    if(progress.bar==TRUE)
+    {
+      if(i %% 100 == 0)
+      {
+        z<-i/nstep
+        zt<-(i-100)/(nstep)
+        polygon(c(zt,zt,z,z), c(1,0,0,1), col="black")
+      }
     }
 
   # calculate jump probabilities without given lamda
@@ -245,7 +248,8 @@ mcmc.popsize <-
     }
     if (i %% thinning == 0& i>burn.in) {count.i<-count.i+1}
   }
-  dev.off()
+ 
+  if(progress.bar==TRUE) dev.off()
 
   list(pos=save.pos,h=save.h,loglik=save.loglik,
        steptype=save.steptype,accept=save.accept)

diff --git a/man/mcmc.popsize.Rd b/man/mcmc.popsize.Rd
index 2952cbc485f81fb7bbc003613eb9d6c331412bf0..5d84e406dfd3505e29f8e1117c60f033f952e16d 100644 (file)
--- a/man/mcmc.popsize.Rd
+++ b/man/mcmc.popsize.Rd
@@ -83,10 +83,10 @@ extract.popsize(mcmc.out, credible.interval=0.95, time.points=200, thinning=1, b
 }
 
 
-\author{Rainer Opgen-Rhein (\url{http://www.stat.uni-muenchen.de/~opgen/}) and
-        Korbinian Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/}).
+\author{Rainer Opgen-Rhein and
+        Korbinian Strimmer (\url{http://strimmerlab.org}).
         Parts of the rjMCMC sampling procedure are adapted from R code by Karl Browman
-        (\url{http://www.biostat.jhsph.edu/~kbroman/})}
+        (\url{http://www.biostat.wisc.edu/~kbroman/})}
 
 \seealso{
 \code{\link{skyline}} and \code{\link{skylineplot}}. }